Hello, I am still having problems understanding how to install mm9 mouse ref genome into our own install of Galaxy. When I try to map with BWA for Illumina the drop down for select ref genome is not populated with anything. How do you grab the mm9 ref file and how do you convert it so that Galaxy local "sees" it? How do you build the index and how do you prepare the loc file? Our install does not contain a folder tool-data/shared/ucsc/builds.txt.
Sorry but I am not a programmer, just a bench scientist. Thanks in advance, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way #2222 Salt Lake City, UT 84108
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